Dec 06, 2023
Version 2
Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS V.2
Peer-reviewed method
- 1R V College of Engineering
- PLOS ONE Lab Protocols
- Spotlight series
External link: https://doi.org/10.1371/journal.pone.0288264
Protocol Citation: M Purushotham Rao, Akshay Uttarkar, Vidya Niranjan 2023. Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS. protocols.io https://dx.doi.org/10.17504/protocols.io.kxygx92rdg8j/v2Version created by Vidya Niranjan
Manuscript citation:
Niranjan V, Rao P, Uttarkar A, Kumar J (2023) Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS. PLOS ONE 18(8): e0288264. https://doi.org/10.1371/journal.pone.0288264
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: December 05, 2023
Last Modified: December 06, 2023
Protocol Integer ID: 91860
Keywords: Martini, Coarse grain, Molecular Simulation, structures for macromolecular simulation, macromolecular simulation, molecular simulation, cg structure, cg model development, cg model, development of cg model, parameterization of the cg model, accuracy of the cg model, grained structure, using gromac, atomistic structure, mapping of the cg, cg, appropriate bead
Abstract
This paper presents a protocol for the development of coarse-grained (CG) structures for macromolecular simulation using the GROMACS software. CG models are widely used in molecular simulations due to their computational efficiency, which allows for the study of large and complex systems. The protocol described here outlines the steps necessary for the creation of CG structures, including the selection of appropriate beads, mapping of the CG beads onto the atomistic structure, and the parameterization of the CG model. The protocol also includes guidelines for validating the accuracy of the CG model, as well as recommendations for future improvements in CG model development. The described protocol will be useful for researchers interested in the development of CG models for macromolecular simulations using GROMACS.
The last step contains a supplemental video with extra context and tips, as part of the protocols.io Spotlight series, featuring conversations with protocol authors.
Guidelines
Commands are indicated in bold letters
Materials
Safety warnings
Ensure all the requirements are satisfied for tools like Gromacs, Dssp.
If there are more warning while running gromas check for their impact, if its not harmful. Ignore it using maxwarn
Before start
A basic understanding on gromacs and simulations.
For visual assistance refer to https://youtu.be/QMR4f4eRSbs
DOWNLOAD NECESSARY PROTEIN
DOWNLOAD THE PDB FILE FROM https://www.rcsb.org/
Preprocess the pdb to remove all ions and B chain or can obtained from here https://drive.google.com/file/d/1YDJV2hKtZ5dJrl8S6A_4AFdTt_lVJFMv/view?usp=sharing
DOWNLOAD NECESSARY SOFTWARE AND FILES
Martinize python script http://cgmartini.nl/index.php/tools2/proteins-and-bilayers/204-martinize
Martini itp file required version http://cgmartini.nl/index.php/force-field-parameters/particle-definitions
Martinin ions itp file http://cgmartini.nl/index.php/force-field-parameters/ions
dssp to ssd python script (Optional) https://github.com/MPurushothamRao/miscellaneous
Gromacs type this in terminal- sudo apt-get install gromacs
Non-polarised water or Polarised water gro files http://cgmartini.nl/index.php/downloads/example-applications/63-pure-water-solvent
XMGRACE type this in terminal- sudo apt-get install grace
Commands shell script https://github.com/MPurushothamRao/miscellaneous
COARSE GRAINING OF PROTEIN
change dssp executable path and required force field and use python3 martinize.py -h for help
python3 martinize.py -f 5y15_processed.pdb -o single-5y15.top -x 5y15-CG.pdb -dssp /usr/local/bin/mkdssp -p backbone -ff martini22
or use ssd file as input
mkdssp -i 5y15.pdb -o 5y15.dssp
to conver dssp file to ssd file
python3 dssp2ssd.py -i 5y15.dssp -o 5y15.ssd
python3 martinize.py -f 5y15_processed.pdb -o single-5y15.top -x 5y15-CG.pdb -ss 5y15.ssd -p backbone -ff martini22
Here we have used second method.
Output of Martinizing (Coarse graining) of the protein
to change name of martini itp file in toplogy, for what you have selected in above step
sed -i -e ‘s/martini.itp/martini_v2.2.itp/’ single-ubq.top
Snap of topology file after above command
SYSTEM SETUP
Setup Periodic box
gmx editconf -f 1UBQ-CG.pdb -o 1UBQ-CG.gro -d 1.0 -c -bt dodecahedron
Output after addition of Box
To minimise the coarse_grained structure in vaccum
gmx grompp -f em_vac.mdp -c 1UBQ-CG.gro -p single-ubq.top -o em_vac.tpr
gmx mdrun -deffnm em_vac -v
After energy minimization in Vacuum
Solvate the protein
gmx solvate -cp em_vac.gro -cs water.gro -radius 0.21 -o solvated.gro
To add number of water molecules into toplogy file for polarised water divide count by 3
cp single-ubq.top system.top
count=$(grep -c “W” solvated.gro | tr -d ‘\n’)
echo -e “\nW $count” >> system.top
Addition of water molecules and making system topology files
Add ions (optional to neutralise or addition ions)
gmx grompp -f ions.mdp -c solvated.gro -p system.top -o ions.tpr
gmx genion -s ions.tpr -o ions.gro -p protein.top -pname NA+ -nname CL- -conc 0.1 -neutral
we have not added here but in the video its shown how to add.
SIMULATION
Energy minimisation
gmx grompp -f em.mdp -c solvated.gro -r solvated.gro -p system.top -o em.tpr -maxwarn 1
maxwarn is because there is an mismatch of atom names but all the atoms are present
gmx mdrun -deffnm em -v
Energy Minimisation
NVT equilibration
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p system.top -o nvt.tpr
gmx mdrun -deffnm nvt -v
NVT equilibration for 20ns
NPT equilibration
gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -p system.top -o npt.tpr
gmx mdrun -deffnm npt -v
NPT equilibration for 20ns
MD run
gmx grompp -f md.mdp -c npt.gro -p system.top -o md.tpr
gmx mdrun -deffnm md -v
`
Production run for 200 ns
ANALYSIS
Analysis
Before analysis conect command should be used to show bonds in visualisation software and also pbc should be removed
echo 1 1 | gmx trjconv -f md.gro -s md.tpr -o recentered_traj.gro -pbc mol -center
echo 1 | gmx trjconv -f recentered_traj.gro -s md.tpr -conect -o connected_traj.pdb
echo 1 1 | gmx trjconv -f md.xtc -s md.tpr -o recentered_traj.xtc -pbc mol -center
sed -i ‘/ENDMDL/d’ connected_traj.pdb
to visualize
vmd recentered_traj.xtc connected_traj.pdb
Video shows protein over 20ns
Calculation RMSD and radius of Gyration and plotting using XMGRACE
echo 1 1 | gmx rms -s md.tpr -f recentered_traj.xtc -o rmsd.xvg
xmgrace rmsd.xvg
echo 1 | gmx gyrate -s md.tpr -f recentered_traj.xtc -o gyrate.xvg
xmgrace gyrate.xvg
RMSD plot Distance nm vs Time ps
Step 2- 12 can be automated using a shell script
sh commands.sh
Video of tutorial
Spotlight video
Protocol references
L. Monticelli, S.K. Kandasamy, X. Periole, R.G. Larson, D.P. Tieleman, S.J. Marrink. The MARTINI coarse grained forcefield: extension to proteins. J. Chem. Theory Comput., 4:819-834, 2008.